Methods for Context Based Compression of Genomic Data for Immuno-Oncology Biomarkers

2. The method of claim 1, wherein the compressing further comprises calculating a mean value of the Nk numbers of reads for the kth category to form the compressed value, wherein the baseline value is a mean baseline value.

3. The method of claim 1, wherein a reduced amount of data for the kth category has a compression ratio of Nk:1.

4. The method of claim 1, wherein the plurality of categories includes a category for an immune inflamed functional context.

5. The method of claim 1, wherein the plurality of categories includes a category for an IFNG signature functional context.

6. The method of claim 1, wherein the plurality of categories includes a category for an immune excluded functional context.

7. The method of claim 1, wherein the plurality of categories includes a category for an immune escape functional context.

8. The method of claim 1, wherein the plurality of categories includes a category for a T cell trafficking functional context.

9. The method of claim 1, wherein the plurality of categories includes a category for an immune desert functional context.

10. The method of claim 1, wherein the step of comparing the compressed value to a baseline value further comprises determining a fold change level in the compressed value compared to the baseline value.

11. The method of claim 10, further comprising assigning a score to the fold change level.

12. The method of claim 11, wherein a greater than 2-fold increase in the fold change level is assigned a score value of +1, a greater than 2-fold decrease in the fold change level is assigned a score value of −1 and fold change levels between the 2-fold decrease and the 2-fold increase are assigned a score value of 0.

14. The method of claim 13, wherein the plurality of assay results includes a TMB result value of high, medium or low, further comprising assigning score values of +1 to the TMB result value of high, 0 to the TMB result value of medium and −1 to the TMB result value of low.

15. The method of claim 13, wherein the plurality of assay results includes a MSI result value of MSI-H (high), MSI-L (low), MSS (stable) or “no data”, further comprising assigning score values of +2 to the MSI result value of MSI-H (high), +1 to the MSI result value of MSI-L (low), 0 to the MSI result value of “no data” and −1 to the MSI result value of MSS (stable).

16. The method of claim 13, wherein the plurality of assay results includes a TCR clonal expansion result of “diverse” or “even”, a TCR convergence result of “evidence of convergence” or “no evidence of convergence”, and a TCR haplotype result, further comprising assigning score values of +1 to the TCR clonal expansion result of “diverse,”−1 to the TCR clonal expansion result of “even,” +1 to the TCR convergence result of “evidence of convergence” and −1 to the TCR convergence result of “no evidence of convergence”.

17. The method of claim 1, further comprising averaging a second set of Nk numbers of reads for the kth category to give the baseline value for the kth category, wherein the second set of Nk numbers of reads correspond to the plurality of targeted genes in normal samples.